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Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Mark W Silby1, Ana M Cerdeño-Tárraga2, Georgios S Vernikos2, Stephen R Giddens3, Robert W Jackson34, Gail M Preston3, Xue-Xian Zhang5, Christina D Moon123, Stefanie M Gehrig3, Scott AC Godfrey133, Christopher G Knight143, Jacob G Malone153, Zena Robinson3, Andrew J Spiers163, Simon Harris2, Gregory L Challis6, Alice M Yaxley7, David Harris2, Kathy Seeger2, Lee Murphy2, Simon Rutter2, Rob Squares2, Michael A Quail2, Elizabeth Saunders8, Konstantinos Mavromatis9, Thomas S Brettin8, Stephen D Bentley2, Joanne Hothersall10, Elton Stephens10, Christopher M Thomas10, Julian Parkhill2, Stuart B Levy1, Paul B Rainey115 and Nicholas R Thomson2*

  • * Corresponding author: Nicholas R Thomson

  • † Equal contributors

Author Affiliations

1 Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA

2 Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

4 School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK

5 New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

6 Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

7 Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

8 DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

9 Genome Biology Program, Department of Energy's Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

10 Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

11 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Auckland, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

12 Current address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand

13 Current address: School of Life Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK

14 Current address: Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK

15 Current address: Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland

16 Current address: SIMBIOS Centre, Level 5, Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK

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Genome Biology 2009, 10:R51  doi:10.1186/gb-2009-10-5-r51

Published: 11 May 2009

Additional files

Additional data file 1:

Supplementary Table 1: Environmentally induced loci in SBW25, and orthologues in Pf0-1 and Pf-5.

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Additional data file 2:

Supplementary Figure 1 shows consensus sequences and HMM logos of P. fluorescens intergenic repeat families. Supplementary Figure 2 shows pie chart analyses of the CDS orientations in the three P. fluorescens strains. Left side, CDSs not flanking intergenic repeats; right side, CDS pairs flanking intergenic repeats. The orientation of the CDSs flanking intergenic repeats has a clear bias to the Tail-repeat-Tail (-> <-) orientation when compared to those CDSs that do not flank intergenic repeats. Supplementary Figure 3 shows the distribution of possible orientations of CDS pairs flanking each repeat sequence family, in (a) SBW25 and (b) Pf0-1.

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Additional data file 3:

Supplementary Table 2 lists P. fluorescens SBW25 ReD coordinates and contents. Supplementary Table 3 lists atypical regions in P. fluorescens SBW25. Supplementary Table 4 lists atypical regions in P. fluorescens Pf0-1.

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